Variant report

Variant	rs1679366
Chromosome Location	chr12:57902627-57902628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57902587-57903358	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:57902487-57902765	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57902586-57902675	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57883464..57886138-chr12:57902032..57904531,3	K562	blood:
2	chr12:57896366..57901111-chr12:57901647..57907518,8	K562	blood:
3	chr12:57881369..57883611-chr12:57902104..57905410,4	MCF-7	breast:
4	chr12:57901367..57904332-chr12:57904666..57906623,2	K562	blood:

Variant related genes	Relation type
MARS	TF binding region
RNU6-594P	TF binding region
ENSG00000123329	Chromatin interaction
ENSG00000252865	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1148550	1.00[EUR][1000 genomes]
rs1284467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2620680	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs537161	1.00[EUR][1000 genomes]
rs59235552	1.00[EUR][1000 genomes]
rs60374392	1.00[EUR][1000 genomes]
rs703833	1.00[EUR][1000 genomes]
rs703840	1.00[EUR][1000 genomes]
rs775325	1.00[EUR][1000 genomes]
rs776340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7973639	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
3	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
4	chr12:57883400-57903000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:57884000-57903200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
7	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
8	chr12:57892800-57908600	Weak transcription	Stomach Mucosa	stomach
9	chr12:57896200-57905400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:57896200-57905600	Weak transcription	NHDF-Ad	bronchial
11	chr12:57898200-57902800	Weak transcription	Hela-S3	cervix
12	chr12:57899000-57905200	Weak transcription	NHLF	lung
13	chr12:57899200-57905000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:57899600-57906400	Weak transcription	Small Intestine	intestine
15	chr12:57899800-57903000	Weak transcription	HUVEC	blood vessel
16	chr12:57900000-57904600	Weak transcription	Right Ventricle	heart
17	chr12:57900000-57905000	Weak transcription	Gastric	stomach
18	chr12:57900000-57905200	Weak transcription	Colonic Mucosa	Colon
19	chr12:57900200-57904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:57900200-57905000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:57900200-57905600	Weak transcription	Esophagus	oesophagus
22	chr12:57900400-57902800	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:57900400-57903000	Weak transcription	Primary T cells from cord blood	blood
24	chr12:57900400-57903000	Weak transcription	Fetal Intestine Large	intestine
25	chr12:57900400-57904000	Weak transcription	Pancreas	Pancrea
26	chr12:57900400-57904200	Weak transcription	Brain Anterior Caudate	brain
27	chr12:57900400-57904600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:57900400-57905000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:57900400-57905400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:57900400-57905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:57900400-57905400	Weak transcription	Ovary	ovary
32	chr12:57900400-57905600	Weak transcription	Fetal Brain Male	brain
33	chr12:57900600-57902800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:57900600-57902800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:57900600-57902800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:57900600-57902800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:57900600-57902800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:57900600-57902800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:57900600-57902800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr12:57900600-57902800	Weak transcription	Fetal Lung	lung
41	chr12:57900600-57902800	Weak transcription	Placenta	Placenta
42	chr12:57900600-57902800	Weak transcription	NH-A	brain
43	chr12:57900600-57902800	Weak transcription	NHEK	skin
44	chr12:57900600-57903000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:57900600-57903000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:57900600-57903000	Weak transcription	Brain Germinal Matrix	brain
47	chr12:57900600-57903000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:57900600-57903000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:57900600-57903000	Weak transcription	A549	lung
50	chr12:57900600-57903000	Weak transcription	GM12878-XiMat	blood

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